Sorry this has been sitting in my inbox for a while - because I wanted
to try to fix it before the next release but I don't think it is going
to happen.

Generically - it doesn't surprise me that Galaxy can handle certain
parameters changing between versions but not conditionals - they are
handled in a much more complex manner. I have updated this
(https://trello.com/c/INCluhxP) Trello card to reference this problem.

Sorry I don't have better news right now.

-John


On Tue, Sep 23, 2014 at 5:54 AM, Peter Briggs
<peter.bri...@manchester.ac.uk> wrote:
> Dear all
>
> One of my users has encountered a problem with extracting a workflow from a 
> history in our local Galaxy installation (tag latest_2014.08.11, changeset 
> 14342:db520d154716).
>
> The history was created with a version of a local tool which has since been 
> updated, and the extraction page warns that the newer version of the tool 
> will be used for those datasets i.e.:
>
> Dataset was created with tool version "0.0.4", but workflow extraction will 
> use version "0.0.7".
>
> However when the extraction is run it fails immediately: the user sees the 
> "Internal Server Error" page, and in the log I see:
> =====
> Error - <type 'exceptions.KeyError'>: 'platform'
> URL: https://galaxy.ls.manchester.ac.uk/workflow/build_from_current_history
> File 
> '/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
>  line 149 in __call__
>   app_iter = self.application(environ, sr_checker)
> File 
> '/home/galaxy/production/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py',
>  line 84 in __call__
>   return self.application(environ, start_response)
> File 
> '/home/galaxy/production/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
>  line 633 in __call__
>   return self.application(environ, start_response)
> File '/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py', 
> line 132 in __call__
>   return self.handle_request( environ, start_response )
> File '/home/galaxy/production/galaxy-dist/lib/galaxy/web/framework/base.py', 
> line 190 in handle_request
>   body = method( trans, **kwargs )
> File 
> '/home/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/workflow.py',
>  line 1220 in build_from_current_history
>   workflow_name=workflow_name
> File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', 
> line 30 in extract_workflow
>   steps = extract_steps( trans, history=history, job_ids=job_ids, 
> dataset_ids=dataset_ids, dataset_collection_ids=dataset_collection_ids )
> File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', 
> line 104 in extract_steps
>   tool_inputs, associations = step_inputs( trans, job )
> File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', 
> line 271 in step_inputs
>   associations = __cleanup_param_values( tool.inputs, param_values )
> File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', 
> line 330 in __cleanup_param_values
>   cleanup( "", inputs, values )
> File '/home/galaxy/production/galaxy-dist/lib/galaxy/workflow/extract.py', 
> line 327 in cleanup
>   group_values = values[input.name]
> KeyError: 'platform'
> =====
>
> 'platform' is a conditional parameter that was introduced into the tool 
> between the two versions. It looks like when tying to use the newer verison 
> of the new tool, that the new parameter is not getting picked up. Is this 
> expected behaviour?
>
> (Btw I've seen a similar issue i.e. the "KeyError: 'platform' exception when 
> I have the two versions of this tool installed from a local toolshed, and try 
> switching between to the newer one from the older one.)
>
> Any help or suggestions are greatly appreciated.
>
> Many thanks
>
> Peter
>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
>
>
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